> thought experiments can't disprove reality

Reality is what it is. If thermodynamics is wrong, it doesn't change reality. It just changes our understanding of reality. Don't be so melodramatic. Once a law/theory is dis-proven there isn't some deja-vu-the-matrix-is-changing-something moment.

At the very least, figuring out where the energy loss is in the system will teach others something, and possibly yourself as well. Thought experiments are where theories come from. Unless you think that theories spring into existence without thought.

{edit} Please don't say, "but I already know about thermodynamics, so there is nothing more for me to learn!" because you would be entirely missing the point.

-- Sir Arthur Stanley Eddington

I suspect most physicists would sooner question their own sanity than question the Second Law, and with good reason.

likewise if we discover a physical phenomenon that violates our current understanding of thermodynamics we don't throw that understanding out. anything that succeeds it needs to explain all the data that it explained + the new stuff.